Has their even been directors who've questioned their own plots?

I've started directing short films wanting to gain more experience, and one thing I noticed about the scripts, written by other writers, is that sometimes I feel their are plot holes but you just go along with it anyway, which is fine of course.

But whenever you hear directors talk about their movies interviews, they seem to know the characters and plotting inside and out. Has their even been a director who is asked a question about the plot in their movie, and they went on record as saying "I have no idea why that character makes that choice, you'll have to ask the writer about that one"?, or something along those lines?

Well, the classic example of this was during the time that Howard Hawks was filming The Big Sleep (1946) with Bogart and Bacall.

While shooting the scene where they are fishing Sternwood's limo out of the bay, Hawks phoned Raymond Chandler to ask him who killed the chauffeur. Surprisingly Chandler said that he didn't know..

N.B. Many believe it was a suicide, since he had been spurned by Carmen Sternwood.

~Doc

I once edited (among other things) a film short and the writer had serious plot holes. When I asked him about it he just told me that he didn't feel people would notice. You may have to find a way to fill in the blanks or abort the project if you don't want to invest all of that effort on a turd.

Oh yeah, that's interesting about the Howard Hawks one.

My latest short film script, written by someone else, has more of a horror torture scenario where the torture chamber is rather elaborate, and the villain is using it to get info out of someone and manipulate them, but I thought a simple, pistol pointed at the head would do, instead of such a SAW series like situation. If that counts as a plot hole, just being unnecessarily over-elaborate.

Why don't you write your own scripts?

One reason is writers will come up with scenes that are very expensive to shoot. If you write what you film, then you can write thinking about just how hard it will be to recreate the scene on film.

Oh I just found that I am not a good writer when it comes to short films, so I rely on others I know and direct their scripts, which they want me to direct anyway, so I thought it was a good arrangement perhaps.

I think the logic here is that a pistol could either not be loaded or even accepted as a quick death by the subject whereas the torture device provides tangible pain and would keep getting used by the villain until the subject either gave up the information or succumbed to a slow and horrible death. That's why I don't think this particular instance counts as a plot hole, but I do agree that if you're going to direct someone else's script you need to ask why it has to unfold the way it does and think about why another option (like using a gun) wouldn't work.

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True, but I thought even torture with a knife would work too like Jack Bauer did, or shoot in the shin, then the thigh, etc. where as the device still seemed elaborate to me, but maybe I'm wrong . The writer just said cause the guy is crazy and sadistic, but since it's a 14 page script that is heavily plot driven already, there wasn't much time to develop that I thought maybe, which is why I didn't see it, but I could be wrong.